getancestors
Class: geneont
Find terms that are ancestors of specified Gene Ontology (GO) term
Syntax
AncestorIDs
= getancestors(GeneontObj
, ID
)
[AncestorIDs
, Counts
]
= getancestors(GeneontObj
, ID
)
... = getancestors(..., 'Height', HeightValue
,
...)
... = getancestors(..., 'Relationtype', RelationtypeValue
,
...)
... = getancestors(..., 'Exclude', ExcludeValue
,
...)
Description
searches AncestorIDs
= getancestors(GeneontObj
, ID
)GeneontObj
,
a geneont object, for GO terms that are ancestors of the GO term(s)
specified by ID
, which is a GO term identifier
or vector of identifiers. It returns AncestorIDs
,
a vector of GO term identifiers including ID
. ID
is
a nonnegative integer or a vector containing nonnegative integers.
[
also
returns the number of times each ancestor is found. AncestorIDs
, Counts
]
= getancestors(GeneontObj
, ID
)Counts
is
a column vector with the same number of elements as terms in GeneontObj
.
Tip
The Counts
return value is useful when you tally counts in gene
enrichment studies.
... = getancestors(..., '
calls PropertyName
', PropertyValue
,
...)getancestors
with optional
properties that use property name/property value pairs. You can specify
one or more properties in any order. Each PropertyName
must
be enclosed in single quotation marks and is case insensitive. These
property name/property value pairs are as follows:
... = getancestors(..., 'Height',
searches up through a specified number of levels, HeightValue
,
...)HeightValue
,
in the gene ontology. HeightValue
is a
positive integer. Default is Inf
.
... = getancestors(..., 'Relationtype',
searches for specified relationship types, RelationtypeValue
,
...)RelationtypeValue
,
in the gene ontology. RelationtypeValue
is
a character vector. Choices are 'is_a'
, 'part_of'
,
or 'both'
(default).
... = getancestors(..., 'Exclude',
controls excluding ExcludeValue
,
...)ID
,
the original queried term(s), from the output AncestorIDs
,
unless the term was reached while searching the gene ontology. Choices
are true
or false
(default).
Input Arguments
GeneontObj | A geneont object, such as created by the geneont constructor function. |
ID | GO term identifier or vector of identifiers. |
HeightValue | Positive integer specifying the number of levels to search upward in the gene ontology. |
RelationtypeValue | Character vector specifying the relationship types to search for in the gene ontology. Choices are:
|
ExcludeValue | Controls excluding ID , the original
queried term(s), from the output AncestorIDs ,
unless the term was reached while searching the gene ontology. Choices
are true or false (default). |
Output Arguments
AncestorIDs | Vector of GO term identifiers including ID . |
Counts | Column vector with the same number of elements as terms in GeneontObj ,
indicating the number of times each ancestor is found. |
Examples
Download the current version of the Gene Ontology database from the Web into a geneont object in the MATLAB® software.
GO = geneont('LIVE', true)
The MATLAB software creates a geneont object and displays the number of terms in the database.
Gene Ontology object with 24316 Terms.
Retrieve the ancestors of the Gene Ontology term with an identifier of
46680
.ancestors = getancestors(GO,46680) ancestors = 8150 9636 17085 42221 46680 50896
Create a subordinate Gene Ontology.
subontology = GO(ancestors) Gene Ontology object with 6 Terms.
Create and display a report of the subordinate Gene Ontology terms, that includes the GO identifier and name.
rpt = get(subontology.terms,{'id','name'}) [ 8150] 'biological_process' [ 9636] 'response to toxin' [17085] [1x23 char] [42221] [1x29 char] [46680] 'response to DDT' [50896] [1x20 char]
View relationships of the subordinate Gene Ontology by using the
getmatrix
method to create a connection matrix to pass to thebiograph
function.cm = getmatrix(subontology); BG = biograph(cm, get(subontology.terms, 'name')); view(BG)
See Also
goannotread
| num2goid
| term